def checkengine(self, engine=None):
if not engine:
opts = {}
engine = choose_engine(opts)
engine.get_input()
engine.script = self
return engine
def checkengine(self, engine=None):
if not engine:
opts = {}
engine = choose_engine(opts)
engine.get_input()
engine.script = self
return engine
def download_public_data(datasets, data_dir='./data/'):
"""Download public datasets using the EcoData Retriever"""
for dataset in datasets:
script_list = SCRIPT_LIST()
opts = get_opts(script_list, args=['install', dataset, '-e', 's', '-f',
'downloaded_data.sqlite'])
script = opts["script"]
engine = choose_engine(opts)
if isinstance(script, list):
for dataset in script:
print "=> Installing", dataset.name
dataset.download(engine, debug=debug)
else:
script.download(engine)
print "Datasets successfully downloaded."
def download_public_data(datasets, data_dir="./data/"):
"""Download public datasets using the EcoData Retriever"""
from retriever import VERSION, SCRIPT_LIST, ENGINE_LIST
from retriever.lib.tools import choose_engine, get_opts
for dataset in datasets:
script_list = SCRIPT_LIST()
opts = get_opts(script_list, args=["install", dataset, "-e", "s", "-f", "downloaded_data.sqlite"])
script = opts["script"]
engine = choose_engine(opts)
if isinstance(script, list):
for dataset in script:
print "=> Installing", dataset.name
dataset.download(engine, debug=debug)
else:
script.download(engine)
print "Datasets successfully downloaded."
def __init__(self, lists):
wx.App.__init__(self, redirect=False)
mfs = wx.MemoryFSHandler()
wx.FileSystem_AddHandler(mfs)
mfs.AddFile("globe.png", icon.GetImage(), wx.BITMAP_TYPE_PNG)
mfs.AddFile("cycle.png", cycle.GetImage(), wx.BITMAP_TYPE_PNG)
mfs.AddFile("download.png", download.GetImage(), wx.BITMAP_TYPE_PNG)
mfs.AddFile("downloaded.png", downloaded.GetImage(),
wx.BITMAP_TYPE_PNG)
mfs.AddFile("error.png", error.GetImage(), wx.BITMAP_TYPE_PNG)
mfs.AddFile("warning.png", warning.GetImage(), wx.BITMAP_TYPE_PNG)
mfs.AddFile("logo.png", logo.GetImage(), wx.BITMAP_TYPE_PNG)
default_connection = get_default_connection()
if default_connection:
parameters = get_saved_connection(default_connection)
parameters["engine"] = default_connection
engine = choose_engine(parameters)
else:
wizard = ConnectWizard(lists, ENGINE_LIST)
success = wizard.RunWizard(wizard.pages[0])
if not success:
wizard.Destroy()
return
engine = wizard.CONNECTION.engine
options = wizard.CONNECTION.option
opts = dict()
for key in options.keys():
opts[key] = options[key].GetValue()
engine.opts = opts
wizard.Destroy()
try:
engine.get_connection()
except:
pass
self.frame = Frame(
None, -1, "EcoData Retriever version %s" % VERSION, lists, engine)
self.frame.Show()
def __init__(self, lists):
wx.App.__init__(self, redirect=False)
mfs = wx.MemoryFSHandler()
wx.FileSystem_AddHandler(mfs)
mfs.AddFile("globe.png", icon.GetImage(), wx.BITMAP_TYPE_PNG)
mfs.AddFile("cycle.png", cycle.GetImage(), wx.BITMAP_TYPE_PNG)
mfs.AddFile("download.png", download.GetImage(), wx.BITMAP_TYPE_PNG)
mfs.AddFile("downloaded.png", downloaded.GetImage(),
wx.BITMAP_TYPE_PNG)
mfs.AddFile("error.png", error.GetImage(), wx.BITMAP_TYPE_PNG)
mfs.AddFile("warning.png", warning.GetImage(), wx.BITMAP_TYPE_PNG)
mfs.AddFile("logo.png", logo.GetImage(), wx.BITMAP_TYPE_PNG)
default_connection = get_default_connection()
if default_connection:
parameters = get_saved_connection(default_connection)
parameters["engine"] = default_connection
engine = choose_engine(parameters)
else:
wizard = ConnectWizard(lists, ENGINE_LIST)
success = wizard.RunWizard(wizard.pages[0])
if not success:
wizard.Destroy()
return
engine = wizard.CONNECTION.engine
options = wizard.CONNECTION.option
opts = dict()
for key in options.keys():
opts[key] = options[key].GetValue()
engine.opts = opts
wizard.Destroy()
try:
engine.get_connection()
except:
pass
self.frame = Frame(None, -1, "EcoData Retriever version %s" % VERSION,
lists, engine)
self.frame.Show()
def download_public_data(datasets, data_dir='./data/'):
"""Download public datasets using the EcoData Retriever"""
from retriever import VERSION, SCRIPT_LIST, ENGINE_LIST
from retriever.lib.tools import choose_engine, get_opts
for dataset in datasets:
script_list = SCRIPT_LIST()
opts = get_opts(script_list,
args=[
'install', dataset, '-e', 's', '-f',
'downloaded_data.sqlite'
])
script = opts["script"]
engine = choose_engine(opts)
if isinstance(script, list):
for dataset in script:
print "=> Installing", dataset.name
dataset.download(engine, debug=debug)
else:
script.download(engine)
print "Datasets successfully downloaded."
}
}
SCRIPT_LIST = SCRIPT_LIST()
TEST_ENGINES = {}
IGNORE = [
"forest-inventory-analysis", "bioclim", "prism-climate", "vertnet", "NPN",
"mammal-super-tree"
]
IGNORE = [dataset.lower() for dataset in IGNORE]
for engine in ENGINE_LIST:
if engine.abbreviation in engine_test:
try:
opts = engine_test[engine.abbreviation]
TEST_ENGINES[engine.abbreviation] = choose_engine(opts)
except:
TEST_ENGINES[engine.abbreviation] = None
pass
errors = []
for module in MODULE_LIST:
for (key, value) in list(TEST_ENGINES.items()):
if module.SCRIPT.shortname.lower() not in IGNORE:
if value != None:
print("==>", module.__name__, value.name, "..........",
module.SCRIPT.shortname)
try:
module.SCRIPT.download(value)
except KeyboardInterrupt:
pass
def main():
"""This function launches the EcoData Retriever."""
if len(sys.argv) == 1 or (len(sys.argv) > 1 and sys.argv[1] == 'gui'):
# if no command line args are passed, launch GUI
check_for_updates(graphical=False if 'darwin' in platform.platform().lower() else True)
lists = get_lists()
from retriever.app.main import launch_app
launch_app(lists)
else:
# otherwise, parse them
script_list = SCRIPT_LIST()
args = parser.parse_args()
if args.quiet:
sys.stdout = open(os.devnull, 'w')
if args.command == 'help':
parser.parse_args(['-h'])
if hasattr(args, 'compile') and args.compile:
script_list = SCRIPT_LIST(force_compile=True)
if args.command == 'update':
check_for_updates(graphical=False)
script_list = SCRIPT_LIST()
return
elif args.command == 'citation':
if args.dataset is None:
citation_path = os.path.join(os.path.split(__file__)[0], '../CITATION')
print citation_path
with open(citation_path) as citation_file:
print citation_file.read()
else:
scripts = name_matches(script_list, args.dataset)
for dataset in scripts:
print dataset.description
return
elif args.command == 'gui':
lists = get_lists()
from retriever.app.main import launch_app
launch_app(lists)
return
elif args.command == 'new':
f = open(args.filename, 'w')
f.write(sample_script)
f.close()
return
if args.command == 'ls' or args.dataset is None:
import lscolumns
#If scripts have never been downloaded there is nothing to list
if not script_list:
print "No scripts are currently available. Updating scripts now..."
check_for_updates(graphical=False)
print "\n\nScripts downloaded.\n"
script_list = SCRIPT_LIST()
all_scripts = set([script.shortname for script in script_list])
all_tags = set(["ALL"] +
[tag.strip().upper() for script in script_list for tagset in script.tags for tag in tagset.split('>')])
print "Available datasets (%s):" % len(all_scripts)
lscolumns.printls(sorted(list(all_scripts), key=lambda s: s.lower()))
print "Groups:"
lscolumns.printls(sorted(list(all_tags)))
return
engine = choose_engine(args.__dict__)
if hasattr(args, 'debug') and args.debug: debug = True
else: debug = False
scripts = name_matches(script_list, args.dataset)
if scripts:
for dataset in scripts:
print "=> Installing", dataset.name
try:
dataset.download(engine, debug=debug)
dataset.engine.final_cleanup()
except KeyboardInterrupt:
pass
except Exception as e:
print e
if debug: raise
print "Done!"
else:
print "The dataset %s isn't currently available in the Retriever" % (args.dataset)
print "Run 'retriever -ls to see a list of currently available datasets"
from retriever.lib.tools import choose_engine
from retriever import MODULE_LIST, ENGINE_LIST, SCRIPT_LIST
MODULE_LIST = MODULE_LIST()
ENGINE_LIST = ENGINE_LIST()
SCRIPT_LIST = SCRIPT_LIST()
TEST_ENGINES = {}
IGNORE = ["AvianBodyMass", "FIA"]
for engine in ENGINE_LIST:
opts = {}
print "** %s **" % engine.name
opts["engine"] = engine.abbreviation
try:
TEST_ENGINES[engine.abbreviation] = choose_engine(opts)
TEST_ENGINES[engine.abbreviation].get_cursor()
except:
TEST_ENGINES[engine.abbreviation] = None
pass
errors = []
for module in MODULE_LIST:
for (key, value) in TEST_ENGINES.items():
if value and not module.SCRIPT.shortname in IGNORE:
print "==>", module.__name__, value.name
try:
module.SCRIPT.download(value)
except KeyboardInterrupt:
pass
def main():
"""This function launches the Data Retriever."""
if len(sys.argv) == 1:
# if no command line args are passed, show the help options
parser.parse_args(['-h'])
else:
# otherwise, parse them
script_list = SCRIPT_LIST()
args = parser.parse_args()
if args.command == "install" and not args.engine:
parser.parse_args(['install','-h'])
if args.quiet:
sys.stdout = open(os.devnull, 'w')
if args.command == 'help':
parser.parse_args(['-h'])
if hasattr(args, 'compile') and args.compile:
script_list = SCRIPT_LIST(force_compile=True)
if args.command == 'defaults':
for engine_item in engine_list:
print("Default options for engine ", engine_item.name)
for default_opts in engine_item.required_opts:
print(default_opts[0], " ", default_opts[2])
print()
return
if args.command == 'update':
check_for_updates()
script_list = SCRIPT_LIST()
return
elif args.command == 'citation':
if args.dataset is None:
print("\nCitation for retriever:\n")
print(CITATION)
else:
scripts = name_matches(script_list, args.dataset)
for dataset in scripts:
print("\nDataset: {}".format(dataset.name))
print("Citation: {}".format(dataset.citation))
print("Description: {}\n".format(dataset.description))
return
elif args.command == 'new':
f = open(args.filename, 'w')
f.write(sample_script)
f.close()
return
elif args.command == 'reset':
reset_retriever(args.scope)
return
elif args.command == 'new_json':
# create new JSON script
create_json()
return
elif args.command == 'edit_json':
# edit existing JSON script
for json_file in [filename for filename in
os.listdir(os.path.join(HOME_DIR, 'scripts')) if filename[-5:] == '.json']:
if json_file.lower().find(args.filename.lower()) != -1:
edit_json(json_file)
return
raise Exception("File not found")
elif args.command == 'delete_json':
# delete existing JSON script
for json_file in [filename for filename in
os.listdir(os.path.join(HOME_DIR, 'scripts')) if filename[-5:] == '.json']:
if json_file.lower().find(args.dataset.lower()) != -1:
confirm = input("Really remove " + json_file +
" and all its contents? (y/N): ")
if confirm.lower().strip() in ['y', 'yes']:
# raise Exception(json_file)
os.remove(os.path.join(HOME_DIR, 'scripts', json_file))
try:
os.remove(os.path.join(
HOME_DIR, 'scripts', json_file[:-4] + 'py'))
except:
# Not compiled yet
pass
return
raise Exception("File not found")
if args.command == 'ls':
# If scripts have never been downloaded there is nothing to list
if not script_list:
print("No scripts are currently available. Updating scripts now...")
check_for_updates()
print("\n\nScripts downloaded.\n")
script_list = SCRIPT_LIST()
all_scripts = []
for script in script_list:
if script.shortname:
if args.l is not None:
script_name = script.name + "\nShortname: " + script.shortname + "\n"
if script.tags:
script_name += "Tags: " + \
str([tag for tag in script.tags]) + "\n"
not_found = 0
for term in args.l:
if script_name.lower().find(term.lower()) == -1:
not_found = 1
break
if not_found == 0:
all_scripts.append(script_name)
else:
script_name = script.shortname
all_scripts.append(script_name)
all_scripts = sorted(all_scripts, key=lambda s: s.lower())
print("Available datasets : {}\n".format(len(all_scripts)))
if args.l is None:
from retriever import lscolumns
lscolumns.printls(sorted(all_scripts, key=lambda s: s.lower()))
else:
count = 1
for script in all_scripts:
print("%d. %s" % (count, script))
count += 1
return
engine = choose_engine(args.__dict__)
if hasattr(args, 'debug') and args.debug:
debug = True
else:
debug = False
sys.tracebacklimit = 0
if hasattr(args, 'debug') and args.not_cached:
use_cache = False
else:
use_cache = True
if args.dataset is not None:
scripts = name_matches(script_list, args.dataset)
else:
raise Exception("no dataset specified.")
if scripts:
for dataset in scripts:
print("=> Installing", dataset.name)
try:
dataset.download(engine, debug=debug, use_cache=use_cache)
dataset.engine.final_cleanup()
except KeyboardInterrupt:
pass
except Exception as e:
print(e)
if debug:
raise
print("Done!")
else:
print("The dataset {} isn't currently available in the Retriever".format(
args.dataset))
print("Run 'retriever ls to see a list of currently available datasets")
def main():
"""This function launches the Data Retriever."""
if len(sys.argv) == 1:
# if no command line args are passed, show the help options
parser.parse_args(['-h'])
else:
# otherwise, parse them
script_list = SCRIPT_LIST()
args = parser.parse_args()
if args.quiet:
sys.stdout = open(os.devnull, 'w')
if args.command == 'help':
parser.parse_args(['-h'])
if hasattr(args, 'compile') and args.compile:
script_list = SCRIPT_LIST(force_compile=True)
if args.command == 'update':
check_for_updates()
script_list = SCRIPT_LIST()
return
elif args.command == 'citation':
if args.dataset is None:
citation_path = os.path.join(os.path.split(__file__)[0], '../CITATION')
print("\nCitation for retriever:\n")
with open(citation_path) as citation_file:
print(citation_file.read())
else:
scripts = name_matches(script_list, args.dataset)
for dataset in scripts:
print("\nDataset: {}".format(dataset.name))
print("Citation: {}".format(dataset.citation))
print("Description: {}\n".format(dataset.description))
return
elif args.command == 'new':
f = open(args.filename, 'w')
f.write(sample_script)
f.close()
return
elif args.command == 'reset':
reset_retriever(args.scope)
return
elif args.command == 'new_json':
# create new JSON script
create_json()
return
elif args.command == 'edit_json':
# edit existing JSON script
for json_file in [filename for filename in
os.listdir(os.path.join(HOME_DIR, 'scripts')) if filename[-5:] == '.json']:
if json_file.lower().find(args.filename.lower()) != -1:
edit_json(json_file)
return
raise Exception("File not found")
elif args.command == 'delete_json':
# delete existing JSON script
for json_file in [filename for filename in
os.listdir(os.path.join(HOME_DIR, 'scripts')) if filename[-5:] == '.json']:
if json_file.lower().find(args.dataset.lower()) != -1:
confirm = input("Really remove " + json_file +
" and all its contents? (y/N): ")
if confirm.lower().strip() in ['y', 'yes']:
# raise Exception(json_file)
os.remove(os.path.join(HOME_DIR, 'scripts', json_file))
try:
os.remove(os.path.join(
HOME_DIR, 'scripts', json_file[:-4] + 'py'))
except:
# Not compiled yet
pass
return
raise Exception("File not found")
if args.command == 'ls':
# If scripts have never been downloaded there is nothing to list
if not script_list:
print("No scripts are currently available. Updating scripts now...")
check_for_updates()
print("\n\nScripts downloaded.\n")
script_list = SCRIPT_LIST()
all_scripts = []
for script in script_list:
if script.shortname:
if args.l is not None:
script_name = script.name + "\nShortname: " + script.shortname + "\n"
if script.tags:
script_name += "Tags: " + \
str([tag for tag in script.tags]) + "\n"
not_found = 0
for term in args.l:
if script_name.lower().find(term.lower()) == -1:
not_found = 1
break
if not_found == 0:
all_scripts.append(script_name)
else:
script_name = script.shortname
all_scripts.append(script_name)
all_scripts = sorted(all_scripts, key=lambda s: s.lower())
print("Available datasets : {}\n".format(len(all_scripts)))
if args.l is None:
from retriever import lscolumns
lscolumns.printls(sorted(all_scripts, key=lambda s: s.lower()))
else:
count = 1
for script in all_scripts:
print("%d. %s" % (count, script))
count += 1
return
engine = choose_engine(args.__dict__)
if hasattr(args, 'debug') and args.debug:
debug = True
else:
debug = False
sys.tracebacklimit = 0
if args.dataset is not None:
scripts = name_matches(script_list, args.dataset)
else:
raise Exception("no dataset specified.")
if scripts:
for dataset in scripts:
print("=> Installing", dataset.name)
try:
dataset.download(engine, debug=debug)
dataset.engine.final_cleanup()
except KeyboardInterrupt:
pass
except Exception as e:
print(e)
if debug:
raise
print("Done!")
else:
print("The dataset {} isn't currently available in the Retriever".format(
args.dataset))
print("Run 'retriever ls to see a list of currently available datasets")
def main():
"""This function launches the EcoData Retriever."""
if len(sys.argv) == 1 or (len(sys.argv) > 1 and sys.argv[1] == 'gui'):
# if no command line args are passed, launch GUI
check_for_updates(graphical=False if current_platform == 'darwin' else True)
lists = get_lists()
from retriever.app.main import launch_app
launch_app(lists)
else:
# otherwise, parse them
script_list = SCRIPT_LIST()
args = parser.parse_args()
if args.quiet:
sys.stdout = open(os.devnull, 'w')
if args.command == 'help':
parser.parse_args(['-h'])
if hasattr(args, 'compile') and args.compile:
script_list = SCRIPT_LIST(force_compile=True)
if args.command == 'update':
check_for_updates(graphical=False)
script_list = SCRIPT_LIST()
return
elif args.command == 'citation':
if args.dataset is None:
citation_path = os.path.join(os.path.split(__file__)[0], '../CITATION')
print "\nCitation for retriever:\n"
with open(citation_path) as citation_file:
print citation_file.read()
else:
scripts = name_matches(script_list, args.dataset)
for dataset in scripts:
print ("\nCitation: {}".format(dataset.citation))
print ("Description: {}\n".format(dataset.description))
return
elif args.command == 'gui':
lists = get_lists()
from retriever.app.main import launch_app
launch_app(lists)
return
elif args.command == 'new':
f = open(args.filename, 'w')
f.write(sample_script)
f.close()
return
elif args.command == 'reset':
reset_retriever(args.scope)
return
if args.command == 'ls' or args.dataset is None:
# If scripts have never been downloaded there is nothing to list
if not script_list:
print "No scripts are currently available. Updating scripts now..."
check_for_updates(graphical=False)
print "\n\nScripts downloaded.\n"
script_list = SCRIPT_LIST()
all_scripts = []
for script in script_list:
if script.name:
if args.l!=None:
script_name = script.name + "\nShortname: " + script.shortname+"\n"
if script.tags:
script_name += "Tags: "+str([tag for tag in script.tags])+"\n"
not_found = 0
for term in args.l:
if script_name.lower().find(term.lower()) == -1:
not_found = 1
break
if not_found == 0:
all_scripts.append(script_name)
else:
script_name = script.shortname
all_scripts.append(script_name)
all_scripts = sorted(all_scripts, key=lambda s: s.lower())
print "Available datasets : {}\n".format(len(all_scripts))
if args.l==None:
import lscolumns
lscolumns.printls(sorted(all_scripts, key=lambda s: s.lower()))
else:
count = 1
for script in all_scripts:
print ("%d. %s"%(count, script))
count += 1
return
engine = choose_engine(args.__dict__)
if hasattr(args, 'debug') and args.debug:
debug = True
else:
debug = False
scripts = name_matches(script_list, args.dataset)
if scripts:
for dataset in scripts:
print "=> Installing", dataset.name
try:
dataset.download(engine, debug=debug)
dataset.engine.final_cleanup()
except KeyboardInterrupt:
pass
except Exception as e:
print e
if debug: raise
print "Done!"
else:
print "The dataset {} isn't currently available in the Retriever".format(args.dataset)
print "Run 'retriever ls to see a list of currently available datasets"
def main():
"""This function launches the Data Retriever."""
if len(sys.argv) == 1:
# if no command line args are passed, show the help options
parser.parse_args(['-h'])
else:
# otherwise, parse them
script_list = SCRIPT_LIST()
args = parser.parse_args()
if args.command == "install" and not args.engine:
parser.parse_args(['install','-h'])
if args.quiet:
sys.stdout = open(os.devnull, 'w')
if args.command == 'help':
parser.parse_args(['-h'])
if hasattr(args, 'compile') and args.compile:
script_list = SCRIPT_LIST(force_compile=True)
if args.command == 'defaults':
for engine_item in engine_list:
print("Default options for engine ", engine_item.name)
for default_opts in engine_item.required_opts:
print(default_opts[0], " ", default_opts[2])
print()
return
if args.command == 'update':
check_for_updates()
script_list = SCRIPT_LIST()
return
elif args.command == 'citation':
if args.dataset is None:
print("\nCitation for retriever:\n")
print(CITATION)
else:
scripts = name_matches(script_list, args.dataset)
for dataset in scripts:
print("\nDataset: {}".format(dataset.name))
print("Citation: {}".format(dataset.citation))
print("Description: {}\n".format(dataset.description))
return
elif args.command == 'new':
f = open(args.filename, 'w')
f.write(sample_script)
f.close()
return
elif args.command == 'reset':
reset_retriever(args.scope)
return
elif args.command == 'new_json':
# create new JSON script
create_json()
return
elif args.command == 'edit_json':
# edit existing JSON script
json_file = get_script_filename(args.dataset.lower())
edit_json(json_file)
return
elif args.command == 'delete_json':
# delete existing JSON script from home directory and or script directory if exists in current dir
confirm = input("Really remove " + args.dataset.lower() +
" and all its contents? (y/N): ")
if confirm.lower().strip() in ['y', 'yes']:
json_file = get_script_filename(args.dataset.lower())
delete_json(json_file)
return
if args.command == 'ls':
# If scripts have never been downloaded there is nothing to list
if not script_list:
print("No scripts are currently available. Updating scripts now...")
check_for_updates()
print("\n\nScripts downloaded.\n")
script_list = SCRIPT_LIST()
all_scripts = []
for script in script_list:
if script.name:
if args.l is not None:
script_name = script.title + "\nName: " + script.name + "\n"
if script.keywords:
script_name += "Keywords: " + \
str([tag for tag in script.keywords]) + "\n"
not_found = 0
for term in args.l:
if script_name.lower().find(term.lower()) == -1:
not_found = 1
break
if not_found == 0:
all_scripts.append(script_name)
else:
script_name = script.name
all_scripts.append(script_name)
all_scripts = sorted(all_scripts, key=lambda s: s.lower())
print("Available datasets : {}\n".format(len(all_scripts)))
if args.l is None:
from retriever import lscolumns
lscolumns.printls(sorted(all_scripts, key=lambda s: s.lower()))
else:
count = 1
for script in all_scripts:
print("%d. %s" % (count, script))
count += 1
return
engine = choose_engine(args.__dict__)
if hasattr(args, 'debug') and args.debug:
debug = True
else:
debug = False
sys.tracebacklimit = 0
if hasattr(args, 'debug') and args.not_cached:
engine.use_cache = False
else:
engine.use_cache = True
if args.dataset is not None:
scripts = name_matches(script_list, args.dataset)
else:
raise Exception("no dataset specified.")
if scripts:
for dataset in scripts:
print("=> Installing", dataset.name)
try:
dataset.download(engine, debug=debug)
dataset.engine.final_cleanup()
except KeyboardInterrupt:
pass
except Exception as e:
print(e)
if debug:
raise
print("Done!")
else:
print("The dataset {} isn't currently available in the Retriever".format(
args.dataset))
print("Run 'retriever ls to see a list of currently available datasets")
